NewPythonPrograms/MergeShared.py at master · marcsze/NewPythonPrograms · GitHub

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#! python

#MergeShared.py

## Example command line entry:

## python MergeShared.py testset.OTUrep.fasta testset.count_table clusterSetSeqList.fasta cluster.taxonomy

# Load the needed modules for the program

import sys

# Read in a Command arguments for consensus sequence file and a degapped aligned and screened fasta file

# Input other instructions from here

def commandLine():

commands = sys.argv

OTUTestFasta = commands[1]

countsFile = commands[2]

OTURefFasta = commands[3]

TaxFile = commands[4]

return OTUTestFasta, countsFile, OTURefFasta, TaxFile

# Read in necessary data and make two dictionaries

# One will store sequence information and the other will store counts for every sample

def createArrays(OTUTestFasta, countsFile):

# Make the first dictionary that will be used matching OTUs

testOTUs = open(OTUTestFasta, 'r')

x = 1

wholeSequence = []

sequenceName = []

TestOTUsequences = {}

for line in testOTUs:

if x%2 == 0:

goodSequence = line.strip('\n')

wholeSequence.append(goodSequence)

else:

name = line[1:]

nameStrip = name.strip('\n')

sequenceName.append(nameStrip)

x = x + 1

for i in range(len(sequenceName)):

TestOTUsequences[sequenceName[i]] = wholeSequence[i]

# Make the second dictionary that will store the total count information

x = 1

groupNames = []

TestSequenceCount = {}

countTable = open(countsFile, 'r')

for line in countTable:

if x == 1:

y = 0

for i in line.split("\t"):

if y >= 2:

name = i.strip('\n')

groupNames.append(name)

else:

groupNames = groupNames

y = y + 1

x = x + 1

else:

y = 0

tempcount = {}

for i in line.split("\t"):

if y == 0:

seqName = i

elif y >= 2:

name = i.strip('\n')

name = eval(name)

tempcount[groupNames[y-2]] = name

y = y + 1

TestSequenceCount[seqName] = tempcount

return TestOTUsequences, TestSequenceCount

# Create a dictonary for each OTU and consensus sequence

def makeRefFile(OTURefFasta, TaxFile):

reference = open(OTURefFasta, 'r')

x = 1

refSequence = []

for line in reference:

if x%2 == 0:

refSequence.append(line)

else:

refSequence = refSequence

x = x + 1

reference.close()

taxonomy = open(TaxFile, 'r')

otuID = []

x = 0

for line in taxonomy:

if x > 0:

otu, total, taxID = line.split("\t")

otuID.append(otu)

x = x + 1

taxonomy.close()

referenceData = {}

for i in range(len(otuID)):

referenceData[otuID[i]] = refSequence[i]

return otuID, referenceData

# Seperate reference sequences into smaller 25bp parts number of 25bp parts based on size

def seperateReference(otuID, referenceData):

SeperatedDatabase = {}

for i in otuID:

tempStorage = []

sequence = referenceData[i]

seqLength = len(sequence)

DivNum = (seqLength // 25) + 1

x = 0

for j in range(DivNum):

if j == (DivNum-1):

final = sequence[(0+x):]

EndPart = final.strip('\n')

tempStorage.append(EndPart)

else:

tempStorage.append(sequence[(0+x):(25+x)])

x = x + 25

SeperatedDatabase[i] = tempStorage

return SeperatedDatabase

# Level 3 > 98.5% match of all sequence matches

def getThirdMatch(TestOTUsequences, TestSequenceCount, OTUSeperatedDatabase, otuID):

SeperatedDatabase = {}

finalizedCompletedMatch = {}

finalizedUnMatched = {}

# Make a 25 bp key to make searching quicker similar to function seperateReference

for i in TestOTUsequences:

sequence = TestOTUsequences[i]

seqLength = len(sequence)

DivNum = (seqLength // 25) + 1

x = 0

tempStorage = []

for k in range(DivNum):

if k == (DivNum-1):

final = sequence[(0+x):]

EndPart = final.strip('\n')

tempStorage.append(EndPart)

else:

tempStorage.append(sequence[(0+x):(25+x)])

x = x + 25

SeperatedDatabase[i] = tempStorage

# Search each 25bp chunk with the 25bp chunk and log % matching if less than 90% after 7 move on to next sequence

print("Trying to match OTUs...")

for i in SeperatedDatabase:

sequence = SeperatedDatabase[i]

for k in range(len(otuID)):

tempRefKey = OTUSeperatedDatabase[otuID[k]]

x = 0

total = 0

try:

for l in range(13):

tempkeySequence = tempRefKey[l]

try:

if tempkeySequence in sequence[l]:

x = x + 25

#Modify this code to account for changes in the middle of the sequence

else:

testSequence = sequence[l]

y = 0

for nucleotide in range(len(tempkeySequence)):

if tempkeySequence[nucleotide] == testSequence[nucleotide]:

y = y + 1

else:

y = y

if nucleotide == (len(tempkeySequence)-1):

x = x + y

except IndexError:

x = x

total = (x/((l+1)*25))*100

if l == 1 and total <= 80:

break

elif l == 6 and total <= 90:

break

elif l == 12 and total >= 99:

finalizedCompletedMatch[i] = otuID[k]

break

except IndexError:

total = (x/((l+1)*25))*100

if l == 1 and total <= 80:

break

elif l == 6 and total <= 90:

break

elif l == 12 and total >= 99:

finalizedCompletedMatch[i] = otuID[k]

break

if total >= 99: break

if k == (len(otuID)-1) and (i not in finalizedCompletedMatch):

finalizedUnMatched[i] = sequence

return finalizedCompletedMatch, finalizedUnMatched

def main():

# Need to create a way to judge accuarcy of calls

OTUTestFasta, countsFile, OTURefFasta, TaxFile = commandLine()

TestOTUsequences, TestSequenceCount = createArrays(OTUTestFasta, countsFile)

otuID, referenceData = makeRefFile(OTURefFasta, TaxFile)

SeperatedDatabase = seperateReference(otuID, referenceData)

finalizedCompletedMatch, finalizedUnMatched = getThirdMatch(TestOTUsequences, TestSequenceCount, SeperatedDatabase, otuID)

counts = {}

for i in finalizedCompletedMatch:

otu = finalizedCompletedMatch[i]

counts[otu] = counts.get(otu,0) + 1

#print(i, otu)

print(counts)

retrievedOTUList = list(counts.items())

retrievedOTUList.sort()

#print(retrievedOTUList)

print(len(finalizedCompletedMatch), len(finalizedUnMatched))

if __name__ == '__main__': main()

NewPythonPrograms/MergeShared.py at master · marcsze/NewPythonPrograms · GitHub

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